1- copy the SAME54_xplained_pro folder to C:\Program Files (x86)\Atmel\sam-ba_2.16\tcl_lib\
2- replace the boards.tcl file at location C:\Program Files (x86)\Atmel\sam-ba_2.16\tcl_lib\ with the one provided with this folder 
Now you should be able to use sam-ba ui
Both the projects applet as well as the monitor projects are available. 